Limits...
Celsius: a community resource for Affymetrix microarray data.

Day A, Carlson MR, Dong J, O'Connor BD, Nelson SF - Genome Biol. (2007)

Bottom Line: Celsius is a data warehousing system to aggregate Affymetrix CEL files and associated metadata.It provides mechanisms for importing, storing, querying, and exporting large volumes of primary and pre-processed microarray data.It is the largest publicly available source of Affymetrix microarray data, and through sheer volume it allows a sophisticated, broad view of transcription that has not previously been possible.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, 90095, USA.

ABSTRACT
Celsius is a data warehousing system to aggregate Affymetrix CEL files and associated metadata. It provides mechanisms for importing, storing, querying, and exporting large volumes of primary and pre-processed microarray data. Celsius contains ten billion assay measurements and affiliated metadata. It is the largest publicly available source of Affymetrix microarray data, and through sheer volume it allows a sophisticated, broad view of transcription that has not previously been possible.

Show MeSH

Related in: MedlinePlus

A gene network constructed from 3600 most varying human probesets. The hierarchical clustering tree and the heat map of the topologic overlap matrix for the 3600 HG-U133A probesets with the largest coefficients of variation measured across 1078 HG-U133A serial number database identifiers (SNIDs) that were annotated as pathologically normal. The color breaks in the colored annotation bar above the heat map mark annotation groups of probesets based on EASE, and tick marks mark the individual modules of highly interconnected probes before being merged into a single annotation group. Colors, left to right are defined as follows: red, transcription; black, response to biotic stimulus; turquoise, ectoderm development; magenta, regulation of metabolism; blue, nervous system development; green, muscle contraction; dark orchid, digestion; chocolate, organic acid metabolism; brown, acute-phase response; dark khaki, complement activation; orange, pregnancy; yellow, sexual reproduction; midnight blue, mitotic cell cycle; deep sky blue, skeletal development; tan, phosphate transport.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2394754&req=5

Figure 7: A gene network constructed from 3600 most varying human probesets. The hierarchical clustering tree and the heat map of the topologic overlap matrix for the 3600 HG-U133A probesets with the largest coefficients of variation measured across 1078 HG-U133A serial number database identifiers (SNIDs) that were annotated as pathologically normal. The color breaks in the colored annotation bar above the heat map mark annotation groups of probesets based on EASE, and tick marks mark the individual modules of highly interconnected probes before being merged into a single annotation group. Colors, left to right are defined as follows: red, transcription; black, response to biotic stimulus; turquoise, ectoderm development; magenta, regulation of metabolism; blue, nervous system development; green, muscle contraction; dark orchid, digestion; chocolate, organic acid metabolism; brown, acute-phase response; dark khaki, complement activation; orange, pregnancy; yellow, sexual reproduction; midnight blue, mitotic cell cycle; deep sky blue, skeletal development; tan, phosphate transport.

Mentions: Genes with similar expression patterns are thought to be more likely to be functionally associated [29]. They may form structural complexes, participate in the same biochemical pathway, or be regulated by a common transcriptional mechanism. Gene co-expression networks are constructed on the basis of microarray data from the transcriptional response of cells to changing conditions [30,31]. In these networks a node corresponds to an individual probeset-based measurement of a given gene. We constructed such a network of 3,600 probesets with the greatest coefficients of variation measured across 1078 HG-U133A SNIDs that were annotated as pathologically normal using previously described methods [31,32]. We identified 35 modules within this network that correspond to well separated branches of the resulting hierarchical clustering tree. They are visualized as blocks along the diagonal of the topologic overlap matrix (TOM), as shown in Figure 7. The TOM measure uses the neighbor information instead of just their direct connection strength (adjacency) and is thus a robust measure of interconnectedness. This is similar to a gene cluster. More details about the topologic overlap measure, along with a tutorial using freely available R software to construct gene co-expression networks and to identify modules, can be found in the Materials and methods section, below. The parameters and other settings specifically used in this application are listed there for readers to replicate this analysis.


Celsius: a community resource for Affymetrix microarray data.

Day A, Carlson MR, Dong J, O'Connor BD, Nelson SF - Genome Biol. (2007)

A gene network constructed from 3600 most varying human probesets. The hierarchical clustering tree and the heat map of the topologic overlap matrix for the 3600 HG-U133A probesets with the largest coefficients of variation measured across 1078 HG-U133A serial number database identifiers (SNIDs) that were annotated as pathologically normal. The color breaks in the colored annotation bar above the heat map mark annotation groups of probesets based on EASE, and tick marks mark the individual modules of highly interconnected probes before being merged into a single annotation group. Colors, left to right are defined as follows: red, transcription; black, response to biotic stimulus; turquoise, ectoderm development; magenta, regulation of metabolism; blue, nervous system development; green, muscle contraction; dark orchid, digestion; chocolate, organic acid metabolism; brown, acute-phase response; dark khaki, complement activation; orange, pregnancy; yellow, sexual reproduction; midnight blue, mitotic cell cycle; deep sky blue, skeletal development; tan, phosphate transport.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394754&req=5

Figure 7: A gene network constructed from 3600 most varying human probesets. The hierarchical clustering tree and the heat map of the topologic overlap matrix for the 3600 HG-U133A probesets with the largest coefficients of variation measured across 1078 HG-U133A serial number database identifiers (SNIDs) that were annotated as pathologically normal. The color breaks in the colored annotation bar above the heat map mark annotation groups of probesets based on EASE, and tick marks mark the individual modules of highly interconnected probes before being merged into a single annotation group. Colors, left to right are defined as follows: red, transcription; black, response to biotic stimulus; turquoise, ectoderm development; magenta, regulation of metabolism; blue, nervous system development; green, muscle contraction; dark orchid, digestion; chocolate, organic acid metabolism; brown, acute-phase response; dark khaki, complement activation; orange, pregnancy; yellow, sexual reproduction; midnight blue, mitotic cell cycle; deep sky blue, skeletal development; tan, phosphate transport.
Mentions: Genes with similar expression patterns are thought to be more likely to be functionally associated [29]. They may form structural complexes, participate in the same biochemical pathway, or be regulated by a common transcriptional mechanism. Gene co-expression networks are constructed on the basis of microarray data from the transcriptional response of cells to changing conditions [30,31]. In these networks a node corresponds to an individual probeset-based measurement of a given gene. We constructed such a network of 3,600 probesets with the greatest coefficients of variation measured across 1078 HG-U133A SNIDs that were annotated as pathologically normal using previously described methods [31,32]. We identified 35 modules within this network that correspond to well separated branches of the resulting hierarchical clustering tree. They are visualized as blocks along the diagonal of the topologic overlap matrix (TOM), as shown in Figure 7. The TOM measure uses the neighbor information instead of just their direct connection strength (adjacency) and is thus a robust measure of interconnectedness. This is similar to a gene cluster. More details about the topologic overlap measure, along with a tutorial using freely available R software to construct gene co-expression networks and to identify modules, can be found in the Materials and methods section, below. The parameters and other settings specifically used in this application are listed there for readers to replicate this analysis.

Bottom Line: Celsius is a data warehousing system to aggregate Affymetrix CEL files and associated metadata.It provides mechanisms for importing, storing, querying, and exporting large volumes of primary and pre-processed microarray data.It is the largest publicly available source of Affymetrix microarray data, and through sheer volume it allows a sophisticated, broad view of transcription that has not previously been possible.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, 90095, USA.

ABSTRACT
Celsius is a data warehousing system to aggregate Affymetrix CEL files and associated metadata. It provides mechanisms for importing, storing, querying, and exporting large volumes of primary and pre-processed microarray data. Celsius contains ten billion assay measurements and affiliated metadata. It is the largest publicly available source of Affymetrix microarray data, and through sheer volume it allows a sophisticated, broad view of transcription that has not previously been possible.

Show MeSH
Related in: MedlinePlus